The Columbia Genome Center maintains a large collection of small molecules, shRNA, siRNA, and cDNA for screening and assay development. The precise set of molecules that are used in a particular screen can be customized depending on the specific nature and goals of your experiment.

In addition, our staff also has close contact with faculty in the Chemical Probe Synthesis Facility, a shared resource to assist researchers in designing and synthesizing novel small molecule probes for stem cell-related research projects.

The following libraries of molecules are available at the Columbia Genome Center.

Small molecules

The Columbia Genome Center maintains several small molecule libraries, giving researchers a very wide range of options for perturbing biological systems of interest.

Lead Optimized Compound Library (LOC)

The Lead Optimized Compound library contains 10,095 compounds picked by process of elimination, in the lab of Brent Stockwell, from a pool of over 3 million compounds from a variety of commercial libraries (Asinex, Life Chemicals, Enamine, TimTec, InterBioScreen and Chembridge). The LOC features the best compounds available both in terms of pharmacokinetic properties and scaffold diversity.

Library compounds have been filtered for traditional physicochemical descriptors such as the rule of five, rotatable bond count, topological polar surface, and suitable aqueous solubility. Compounds were also evaluated for reactivity and toxicity using published and in-house Columbia Genome Center predictors based on data obtained from previous library screening experiences.

Each compound represents a unique scaffold identified by compound clustering, eliminating duplicates and creating a diverse set of potential lead molecules. To improve hit-to-lead ratios, special emphasis was placed on eliminating scaffolds considered unsuitable for further lead development as well as compounds likely to be acting nonspecifically, such as detergents.

The LOC represents an optimally diverse sampling of the compound pool currently available from commercial vendors.

John Hopkins University Clinical Compound Library (JHCCL)

The Johns Hopkins University Clinical Compound Library contains 1,600 FDA-and foreign-approved drugs in 7 plates. The library is assembled in 384-well plate format carrying 5 mM stocks of drugs.

Spectrum Collection

Created by Microsource Discovery Systems, the Spectrum Collection contains 2,320 biologically active and structurally diverse compounds from its libraries of known drugs, experimental bioactives, and pure natural products.

Prestwick Chemical Library

The Prestwick Chemical Library contains 1,200 small molecules, all of which are in FDA-approved drugs.

siRNA

The Columbia Genome Center maintains a variety of Dharmacon siGENOME® SMARTPool® siRNA libraries, including:

• Human Genome
• Human Drug Targets
• Human G Protein-Coupled Receptor
• Human Ion Channel
• Human Phosphatase
• Human Protease
• Human Protein Kinase’
• Human Ubiquitin Conjugation Subsets 1 to 3
• shRNA

Researchers at Columbia University have exclusive access to the Sigma Aldrich Mission shRNA collection. The mission collection is derived from the RNAi Consortium (TRC), a public-private effort based at the Broad Institute that has produced a human genome-wide lintiviral short hairpin RNA (shRNA) library for testing human and mouse genes.

cDNA

The Precision LentiORFs collection (Thermo Scientific) is a library of human full-length expression-ready lintiviral open reading frames (ORFs) generated using gene content from the fully sequenced ORFeome Collaboration Collection. For more information see the Precision LentiORF Technical Manual.